Cocoa is known as an important source of flavan-3-ols, but their fate “from the bean to the bar” is not yet clear. Here, procyanidin A2 found in native cocoa beans (9–13 mg/kg) appeared partially epimerized into A2E1 through fermentation, whereas a second epimer (A2E2) emerged after roasting. At m/z 575, dehydrodiepicatechin A was revealed to be the major HPLC peak before fermentation, whereas F1, a marker of well-conducted fermentations, becomes the most intense after roasting. RP-HPLC-ESI(−)-HRMS/MS analysis performed on a procyanidin A2 model medium after 12 h at 90 °C revealed many more degradation products than those identified in fermented cocoa, including the last epimer of A2, A2 open structure intermediates (m/z 577), and oxidized A-type dimers (m/z 573).